Blog

coSMicQC: A step toward quality control and improvement of morphology profiles

Let’s tour the single-cell morphological galaxy with coSMicQC! Hi everyone! 🤩 I’m back with another blog post! This time, I want to share something I’ve become very excited and passionate about: ✨ Quality control of single-cell morphology profiles ✨ I will go over what is quality control for morphology profiles, existing work on this topic, the software (coSMicQC) that we have developed to help in this area, and where we hope to go from here. Contents 📋 What is quality control for s...

Steps for Performing Illumination Correction in Microscopy Images

The Process of Illumination Correction on Microscopy Images Hello again! 👋 It has been a little while since the last blog post! But, I am excited to be writing this new and updated blog post stemming from my first blog post ever on illumination correction (IC). I have grown and learned a lot in my first year of my position, from CellProfiler pipelines to multi-processing. After all the experience I have gained, I believe it is the right time to make an updated blog post on the fun concept o...

Segmentation Software Usability and Performance: Part I

A Brief Comparison of Popular Cell Segmentation Software Welcome back! I hope that you were able to come up with an amazing illumination correction pipeline from my illumination correction blog post and are ready for segmentation! If you are just starting with this blog post, then welcome in! As a reminder from my previous post, keep in mind that any method or software you use in your pipeline might not be optimal or might not contain the functionalities that you want (e.g. model training,...

Illumination Correction Made Easier

Illumination Correction: A Comparison of Methods For anyone new to cell-image analysis (like me!), let me preface this blog post with the fact that no matter how good a method is, nothing will ever be “perfect.” In this field, the main goal is to try and minimize any issues within the images that you have. Examples of issues include blurry/noisy images, imperfect segmentation, uneven illumination (the main point of this blog), among others. Being able to interpret if the method you chose w...

Microscopy data playbook

A suitable and flexible data management strategy is essential for effective and trustworthy science. Our goal for data is to maximize access, understanding, analysis speed, and provenance while reducing barriers, unnecessary storage bloat, and cost. Data perspectives We think about data using three different perspectives: Level Origin Flow Each perspective requires us to think through different considerations for storage, access, and provenance management. Managing microscopy dat...

Day 0 in the Way Lab

Today, September 15th, 2021, is Day 0 of the Way Lab @ CU Anschutz in the brand new Center for Health AI. While I’m writing this post from my kitchen table, WFH, still surrounded by moving boxes, I am very excited for this new chapter and to kick off my research group. The first blog post will be more of a public journal entry than a traditional blog post (whatever that means). But as I sit in my new Denver apartment, I am asking myself “What do I do now?”. I’ll try to answer this Q below,...